Amatur Rahman

Selection scans and downstream analysis with selscan

The paper introduces enhanced features in selscan v3.0 for analyzing selection signals using EHH statistics and demonstrates their application on simulated and real genomic data.

EGGS: Empirical Genotype Generalizer for Samples

EGGS generates empirical genotype data with missing values by replicating genotype distributions across segments, offering tools for data manipulation and format conversion.

Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans

The paper introduces a dynamic programming algorithm that improves the speed and memory efficiency of EHH-based selection scans for large-scale genomic datasets.

Evolutionary Influences on Local Patterns of Genetic Relatedness

The paper introduces LODESTAR, a method to analyze local genetic relatedness patterns using Procrustes Analysis, to identify selection regions and inverted segments.

Compression algorithm for colored de Bruijn graphs

The paper introduces a new compression tool for colored de Bruijn graphs, achieving better compression than existing tools across various datasets.

Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful

This paper identifies theoretical and practical issues with unitig-based genome assembly, showing that unitigs can be unsafe and lead to under-assembly even with error-free data.

Representation of k-mer sets using spectrum-preserving string sets

The paper introduces a method to efficiently represent k-mer sets using spectrum-preserving string sets, achieving better compression and indexing than existing tools.

kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9

kRISP-meR designs CRISPR/Cas9 guide RNAs without a reference genome, achieving specificity similar to reference-based tools.